final commit for ape 3.0-8

[ape.git] / man / ltt.plot.Rd

diff --git a/man/ltt.plot.Rd b/man/ltt.plot.Rd
index b40cf1e4d4f04a124860f65d5d82ae2a08307b8b..9af111642be9e92529a2ed0b4c16f91e0ac2ecac 100644 (file)
--- a/man/ltt.plot.Rd
+++ b/man/ltt.plot.Rd
@@ -57,8 +57,8 @@ ltt.plot.coords(phy, backward = TRUE, tol = 1e-6)
 
   The option \code{tol} is used as follows: first the most distant tip
   from the root is found, then all tips whose distance to the root is
 
   The option \code{tol} is used as follows: first the most distant tip
   from the root is found, then all tips whose distance to the root is

-  not more different from the previous one than \code{tol} are
-  considered to be contemporaneous with it.
+  not different from the previous one than \code{tol} are considered to
+  be contemporaneous with it.

 
   If the tree is not ultrametric, the plot is done assuming the tips,
   except the most distant from the root, represent extinction events. If
 
   If the tree is not ultrametric, the plot is done assuming the tips,
   except the most distant from the root, represent extinction events. If


@@ -73,8 +73,11 @@ ltt.plot.coords(phy, backward = TRUE, tol = 1e-6)
   \code{"phylo"} (single trees) and/or \code{"multiPhylo"} (multiple
   trees). Any number of objects may be given. This function is mainly
   for exploratory analyses with the advantages that the axes are set
   \code{"phylo"} (single trees) and/or \code{"multiPhylo"} (multiple
   trees). Any number of objects may be given. This function is mainly
   for exploratory analyses with the advantages that the axes are set

-  properly to view all lines, and the legend is plotted by default. For
-  more flexible settings of line drawings, it may be better to combine
+  properly to view all lines, and the legend is plotted by default. The
+  plot will certainly make sense if all trees have their
+  most-distant-from-the-root tips contemporaneous (i.e., trees with only
+  extinct lineages will not be represented properly). For more flexible
+  settings of line drawings, it may be better to combine

   \code{ltt.plot()} with successive calls of \code{ltt.lines()} (see
   examples).
 
   \code{ltt.plot()} with successive calls of \code{ltt.lines()} (see
   examples).
 


@@ -101,9 +104,9 @@ ltt.plot.coords(phy, backward = TRUE, tol = 1e-6)
 }
 \author{Emmanuel Paradis}
 \seealso{
 }
 \author{Emmanuel Paradis}
 \seealso{

-  \code{\link{skyline}}, \code{\link{branching.times}},
-  \code{\link{birthdeath}}, \code{\link{bd.ext}},
-  \code{\link{yule.cov}}, \code{\link{bd.time}};
+  \code{\link{kronoviz}}, \code{\link{skyline}},
+  \code{\link{branching.times}}, \code{\link{birthdeath}},
+  \code{\link{bd.ext}}, \code{\link{yule.cov}}, \code{\link{bd.time}};

   \code{\link[graphics]{plot}} for the basic plotting function in R
 }
 \examples{
   \code{\link[graphics]{plot}} for the basic plotting function in R
 }
 \examples{